a Schematic depiction of skeletal muscle anatomy. b Bar plots and UMAP visualization (gray, low; red, high expression) showing examples of genes with cell subtype-specific expression (arrow). c Immunofluorescence staining of skeletal muscle from PdgfraH2BGFP reporter line for THBS4 and PECAM1. d RNAscope staining for Pdgfra, Col12a1, and Dcn. e UMAP visualization with pagoda2 clusters annotated and indication of cells specifically analyzed with SPIN. f Expression heat map (loess smoothed (locally weighted scatterplot smoothing) values; blue, low; yellow high) of 97 genes in the ECM + matrisome gene-set (upper) and 228 additional genes (lower) of the perimysial cells SPIN range (see also Online Supplementary Data 7). Bar plots showing examples of perimysial differentially expressed genes (arrows; Wif1, Col22a1, Chodl, and Rflnb) color coded based on pagoda2 clustering (# 2, 9). g Immunofluorescence staining of skeletal muscle from PdgfraH2BGFP reporter line for POSTN and PECAM1 (consecutive section to c). Arrowheads: perimysial cells (PM); arrows: paramysial cells (PaM). h UMAP visualization, color coded for cellular origin according to muscle subtype (M. soleus, M. gastrocnemius or undefined), and pagoda2 clusters annotated. Arrow indicates pagoda2 cluster 4, which is enriched in cells specifically captured from soleus muscle (upper panel). Bar plots and UMAP showing examples of cluster four enriched genes (arrows; C1qtnf3 and Cthrc1). Scale bar: c, g 200 µm, d 100 µm.